R Markdown

This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see http://rmarkdown.rstudio.com.

When you click the Knit button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

summary(cars)
##      speed           dist       
##  Min.   : 4.0   Min.   :  2.00  
##  1st Qu.:12.0   1st Qu.: 26.00  
##  Median :15.0   Median : 36.00  
##  Mean   :15.4   Mean   : 42.98  
##  3rd Qu.:19.0   3rd Qu.: 56.00  
##  Max.   :25.0   Max.   :120.00
library('ggplot2')
  library('plotly')
## 
## Attaching package: 'plotly'
## The following object is masked from 'package:ggplot2':
## 
##     last_plot
## The following object is masked from 'package:stats':
## 
##     filter
## The following object is masked from 'package:graphics':
## 
##     layout
  setwd('~/mygraph2/bin/')  
mygenes <- read.csv('gene_dist_head.tsv', header= TRUE, sep = "\t",fill = TRUE) 
autosomes<-c("1","2","3","4","5","6","7","8","9","10",
  "11","12","13","14","15","16","17","18","19","20","21","22")  
genes<- mygenes[ which(mygenes$chr %in% autosomes), ]
genes$chr <- factor(genes$chr, levels = autosomes) 
ggplot(data = genes) +  geom_bar(mapping = aes(x = chr, fill = feature), width = 1)

ggplot(data = genes) +
 geom_bar(mapping = aes(x = chr, fill = feature), width = 1) +
 coord_polar()

p<-ggplot(data = genes) + 
    geom_bar(mapping = aes(x = chr, fill = feature), width = 1) 
  ggplotly(p)

Including Plots

You can also embed plots, for example:

Note that the echo = FALSE parameter was added to the code chunk to prevent printing of the R code that generated the plot.